[gmx-users] Gromacs on an IBM Power8

Szilárd Páll pall.szilard at gmail.com
Wed Sep 28 19:40:39 CEST 2016


Brief notes/recommendations:
- Use the recently released fftw 3.3.5, it has VSX support
(contributed by us, that is by Erik Lindahl)
- Use at least gcc 5.x, it's significantly faster.
- 8 threads/core will never be optimal, 2-4 is best; currently the
best way to do that is to use -pinstride
- 1 rank/core is rarely optimal (with GPUs), IIRC from when I last ran
on the 2x12c IBM machines, 6-8 ranks were a good balance.

Finally, when it comes to performance, Intel and AVX2 will be hard to
beat with the current Power8 chips, but with GPUs combined, we've
showed such machines match/beat Haswell, e.g see
(slide 34)


On Wed, Sep 28, 2016 at 4:04 PM, Baker D.J. <D.J.Baker at soton.ac.uk> wrote:
> Hello,
> I would appreciate advice on running gromacs on a Power8 machine, please. I recently downloaded and installed gromacs v2016 on one of our IBM Power8 machines. I understand that this version of gromacs has support for Power8 machines and it certainly performs a great deal better than earlier versions. So that is progress. On the other hand I wonder if the Power8 could do better. I used one of the gromacs benchmarks (case A) supplied by PRACE and ran the following command on the Power8..
> gmx mdrun -ntomp 8 -ntmpi 24 -s ion_channel.tpr -maxh 0.50 -resethway -noconfout -nsteps 10000 -g logfile -nb cpu
> In other words there are 24 cores and I turned on SMT=8. Using that configuration and the above command the performance is about the same as on a 16 core Sandybridge node...
> Performance in ns/day
> SandyBridge (16 cores) - 11.23
> Power8 (24 cores)          -- 11.82
> Power8 (using 2 gpus)  -- 28.34
> That's compiling with the GNU compiler v4.9.1. Should I be able to do better on the Power8 with a different/later compiler and/or different runtime settings?
> Best regards,
> David
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